Nitabird, use your windows 98 boot disk and format both drives from a dos prompt. This is the fastest and easiest way. You will need to Fdisk (repartition) the drive and enable both for large hard drive support though (FAT 32) as you won't be able to format that large drive as FAT 16.

You may also want to reconsider using the smaller drive as the boot drive, unless there is a specific reason for doing so. The larger drive should be faster, therefore it will give you better performance.